In what would soon become Israel, Vilner was disenchanted with the politics, claiming that the hatred directed at Jews in Vilna was now directed at the Arabs. He joined the Palestine Communist Party (PCP), which accepted Arab and Jewish membership, but supported partition. Vilner criticized both the British and Israeli government, but justified signing the Israeli Declaration of Independence on the grounds that this would eliminate another British colony. Besides, the PCP stressed that the Charter contained a promise to help implement the UN resolutions providing for two independent states, Israel and Arab Palestine, and to uphold full equality and civil liberties for all Israeli citizens.[2]

In 1949, he was elected to the Knesset as a member of Maki. He resigned from the Knesset in December 1959, six weeks after the 1959 elections, but was re-elected in 1961. However, he resigned again two months after the 1961 elections.

In 1965 Vilner and several other Maki members broke away from the party to form Rakah following disagreements about the Soviet Union's increasingly anti-Israeli stance (Vilner was on the USSR's side), and was elected to the Knesset on the new party's list in the 1965 elections.

On June 5, 1967, Vilner was the sole Jewish deputy (joined only by fellow Communist Party of Israel deputy Tawfik Toubi) to speak out in the Knesset against Israel's preemptive strike against an imminent Egyptian invasion. Calling that day the darkest in Israel's history, Vilner demanded an immediate halt to the Israeli invasion of Arab-occupied lands. Vilner stressed that there was no other way to solve the conflict between Israel and its neighbors but mutual recognition of the national rights of Israelis and Arabs, including the right of the Palestinians to self-determination and independent statehood. On October 15, he was badly wounded by a member of the right-wing party Gahal.[4][5]

Rakah became part of Hadash before the 1977 elections, and Vilner remained an MK until 1990 when he resigned as part of a seat rotation agreement, making him the third longest serving after Tawfik Toubi and Shimon Peres.

He was married to Esther Vilenska, another Israeli communist politician but divorced later, after having two sons together. His cousin Abba Kovner was a well-known Israeli poet.

Vilner was buried in the Yarkon Cemetery, Tel Aviv, beside the grave of his life companion Golda Ita Vilner (1903 - 2000). He is survived by two sons and two grandchildren.